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NMR processing:
MDD
NMR assignment:
Backbone:
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MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Old 09-21-2008, 02:27 AM
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Default Postdoctoral position at Vanderbilt in Structural Biology of DNA Repair

Vanderbilt University's Center for Structural Biology are looking for a postdoc to study the structures of DNA repair machinery (found at http://www.icmrbs2008.org )

Quote:
Post-Doctoral Position Available

A postdoctoral position is available as part of the large multi-investigator Structural Biology of DNA Repair Machinery (SBDR) program. SBDR is funded by the National Cancer Institute and supports multi-institutional teams of investigators at more than 10 universities across the US and one in the Netherlands. Our laboratory is the sole NMR lab in the SBDR and has both lab-centered and collaborative projects with SBDR and other investigators. Many projects involve the eukaryotic ssDNA binding protein, replication protein A (RPA), which is a 116 kDa heterotrimer containing 8 structural/functional domains. NMR is used to map binding sites between domains of RPA and other DNA replication and repair proteins such as DNA primase, SV40 large T antigen, ATRIP, Rad9, Mre11, and others. These studies are fully integrated with functional studies in vitro and in vivo. As part of the effort to understand the action of DNA replication and repair machinery, NMR, modeling and SAXS are used to characterize the dynamic architecture of full-length RPA and the remodeling of its architecture as the protein binds ssDNA and other proteins. Interested candidates should send a cover letter and CV to: walter.chazin@vanderbilt.edu.
http://structbio.vanderbilt.edu/chazin/position.html
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